Contacts of the strand formed by residues 2005 - 2010 (chain E) in PDB entry 1PDW
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ARG2005 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2003E SER 4.1 8.1 - - - +
2004E LYS* 1.3 77.5 - - - +
2006E ALA* 1.3 60.9 + - - +
2031E ILE* 4.5 1.1 - - - -
2032E LYS* 3.2 31.2 - - + +
2034E THR* 6.0 1.3 - - - +
2064E GLU* 2.8 45.1 + - - +
2065E GLY* 3.5 10.3 - - - -
2066E PRO* 3.0 26.6 + - - +
2067E TYR* 3.6 22.7 - - + +
2068E ASP* 2.9 36.8 + - - +
2069E VAL* 3.5 4.1 + - - -
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Residues in contact with ALA2006 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2005E ARG* 1.3 74.1 - - - +
2007E LEU* 1.3 61.7 + - - +
2008E VAL 4.1 0.4 - - - -
2026E MSE 3.7 28.5 - - + -
2031E ILE* 4.2 9.8 - - + +
2032E LYS 2.9 8.8 + - - +
2033E VAL* 3.5 5.8 - - + -
2034E THR* 2.8 28.4 + - - -
2067E TYR* 3.6 5.8 - - - -
2069E VAL* 3.4 26.2 - - + -
2071E VAL* 4.9 1.8 - - + -
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Residues in contact with LEU2007 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2006E ALA* 1.3 71.9 - - - +
2008E VAL* 1.3 54.9 + - - +
2009E ILE* 3.9 11.1 + - + -
2034E THR* 3.7 7.0 - - - +
2036E ALA* 3.5 32.1 - - + -
2058E LEU* 4.1 15.9 - - + -
2061E ALA* 3.9 15.9 - - + +
2062E LYS* 5.4 2.2 - - - -
2067E TYR* 3.5 40.1 - - + -
2069E VAL 3.0 10.2 + - - +
2070E VAL* 3.4 8.9 - - + +
2071E VAL* 2.8 32.4 + - - +
2091E ILE* 4.2 24.7 - - + -
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Residues in contact with VAL2008 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2007E LEU* 1.3 75.3 - - - +
2009E ILE* 1.3 62.7 + - - +
2010E LEU 3.3 1.4 + - - +
2019E THR* 4.2 19.1 - - + +
2022E PRO* 5.8 0.7 - - + -
2023E VAL* 4.0 10.8 - - + -
2026E MSE 3.8 20.4 - - + -
2033E VAL* 3.7 25.4 - - + -
2034E THR 3.0 11.1 + - - +
2035E VAL* 3.7 9.8 - - + +
2036E ALA 2.9 26.8 + - - -
2071E VAL* 3.6 17.0 - - + +
2073E PRO* 4.0 23.6 - - + -
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Residues in contact with ILE2009 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2007E LEU* 4.4 9.2 - - + -
2008E VAL* 1.3 70.5 - - - +
2010E LEU* 1.3 61.5 + - - +
2011E ALA 3.8 2.1 + - - -
2036E ALA* 3.7 5.6 - - - +
2038E LEU* 4.3 17.0 - - + -
2058E LEU* 4.1 17.3 - - + -
2070E VAL* 4.3 13.2 - - + -
2071E VAL 3.2 11.4 + - - +
2072E LEU* 3.9 19.1 - - + -
2073E PRO* 3.3 22.8 - - - +
2082E LEU* 3.3 29.3 - - + +
2088E VAL* 3.9 29.2 - - + -
2091E ILE* 4.3 19.7 - - + -
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Residues in contact with LEU2010 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2008E VAL* 3.3 1.5 + - - +
2009E ILE* 1.3 71.1 - - - +
2011E ALA* 1.3 62.0 + - - +
2014E ALA* 3.7 25.8 - - + -
2019E THR* 4.2 20.2 - - + +
2035E VAL* 3.9 28.0 - - + -
2036E ALA 2.8 15.4 + - - +
2037E GLY* 3.6 2.6 - - - -
2038E LEU* 2.9 26.2 + - - -
2039E ALA 4.8 0.2 + - - -
2044E VAL* 3.7 36.8 - - + +
2046E CYS* 4.2 9.4 - - - -
2052E ILE* 4.1 23.3 - - + +
2054E PRO* 4.7 5.2 - - + -
2073E PRO* 5.5 0.4 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il